1. Introduction

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This document was inspired by noticing the convergence of artificial intelligence with ecological research and the ground breaking development of the BirdNET algorithm developed by Dr. Stefan Kahl with the K. Lisa Yang Center for Conservation Bioacoustics at the Cornell Lab of Ornithology. BirdNET Paper.

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Birdnet is an machine learning model developed using the tensorflow algorithm, which is a software library developed by Google to be used to develop AI models that can make predictions based on a large dataset of pre-trained data. Birdnet is trained based on hundreds of thousands of bird calls from Cornell Lab of Ornithology across various species, and can provide predictions for around 3,000 bird calls worldwide (as of 2023). To simply put it, if you have an audio file with various bird calls, BirdNET can be used to identify which species are calling in the given audio-file, at which time of the audio, and to what degree it believes that species to be. If you think you want to have this software available, this document is going to show you the steps I have developed to streamline a weeks worth of audio files to be processed to see which species occur in a given area.

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Now, before I explain my process, I want to highlight some alternatives that can be done with BirdNET. BirdNET was developed in Python, therefore, if you have a real foundation in the Python language, I encourage you to explore Dr. Kalh’s github repository. In the github repo, Dr, Kahl explains how one would set up the python environment and run the model through either Ubuntu or Windows. There is an option to use a GUI he developed to run BirdNET on your audio files, but if you want to run multiple files with one command, compile the results into one table, and have validation tools to check predictions, I encourage you to explore my option. Finally, within Dr. Kahl’s github repository, he provides other projects that have used BirdNET to identify birds in real time from ARU units.The only issue with these projects is that they require LTE connectivity, therefore, not the greatest help for a typical biological ARU survey.

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If you have decided to go through my alternative framework on how I have been using BirdNET for both species investigation and potential incorporation to ESA surveys, below I will run a step-by-step process from recording the data from the field to processing the audios on my Windows Laptop.

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The only pre-requisites required for my framework is a general understanding of the R language and Git, which for most young biologists that have went through Graduate School, should have a fundamental understanding. If you are one who is not familiar with R & Rstudio, I suggest you watch this quick video..

2. The Framework

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1. Deploy Autonomous Recording Units (ARUs) into the field of study.

2. Download the audio recordings to the computer

3. Set-up BirdNET with the birdnetlib conda package.

4. Run your modified version of the “bird_scanner.R” R script from the Bird-Scanner Repository.

5. Check predictions using the “bird-checker.R” script

3. Deploying ARUs

An autonomous recording unit, otherwise known as an ARU, is a self-contained audio recording device that is deployed in marine or terrestrial environments for bioacoustic monitoring. The unit is used in both marine and terrestrial environments to track the behavior of animals, identify sensitive species occurring in an area, gauge habitat quality, and monitor the ecosystems.

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Within the last two decades, ARUs have been growing in popularity for use in studies on birds, cetaceans, primates, bats, anurans, and insects. However, for most of the history of deploying these ARUs into the field, would require costly (>$1,000) units and long hours of downloading and processing the audio data into distilling down where species were calling based on known experience of species specific calls.

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With the advancements in the bioacoustic industry today, and manufacturing overall, the costs associated with ARUs has drastically decreased for the entry-level devices (<$300). The three big players of the bioacoustic ARUs that I recommend using are Wildlife Accoustics, Open Acoustics Audiomoths, and SwiftOne by Cornell Labs.

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My firm has obtained two ARU devices that I would recommend as a staring point with Bird-Scanner; the Audiomoth v1.2.0, which is a relatively cheap (<$150) audio device that has a bit of a learning curve, but was my go to device for deployment for the entire 2022 field season.

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The other device was from Wildlife Acoustics: Song Meter Micro, which was simple to set up and has an app to configure the recording times. The device retails for $250, which is a bump up in price compared to the Audiomoth, however, these devices are backed by a greatly reputable company.

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For this walk through on Bird-Scanner, I deployed an ARU in my backyard under my bird feeder, which was set up to start recording from 6:00 - 19:00 and recorded a 5 minute segment of audio every 15 minutes, which equates to 52 wav files for the day. At the end of a recording session, at the birdfeeder, I walked out to the device, popped it open, then removed the SD card, and plugged the card into my laptop.

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Currently, I have only deployed Bird-Scanner at 12 locations across the Navajo Nation during habitat assessment surveys to assist in determining species that occur within or near the project area. So far Bird-Scanner has improved my detection ability of birds for my project (which, are the addition of birds identified by Bird-Scanner from the birds I am observing while conducting the survey) reports by 25%.

4. Download Audio Data

To download the wav files from the ARU, plug the micro-SD card from the device into your computer, and transfer the files over into a folder of your choice (personally, I would save them under the data folder in the Bird-Scanner repository (refer to section 5).

5. BirdNET and birdnetlib

To set up BirdNET on your laptop, the minimum requirements you will need is a general understanding of conda environments and how they interact with r-reticulate package, which I will walk you through. I will try to make this process as simple as possible, but reach out to me if you get stuck. One of the issues with BirdNET is that it was originally designed to run results on one file at a time, tailored to be run in the windows terminal, and therefore, lacks the data management power that R clearly as a researcher application. So to bring the best of both worlds, I chose to develop my workflow with R leveraging the great birdnetlib conda package.

Below, I will show you my process on how to set up BirdNET to run with this repository.

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A) First, Go ahead and download Anaconda for Windows. Following the download you will need to open the “Anaconda Prompt” terminal.

In the terminal run the following commands:

conda create -n pybirdanalyze python=3.7

This creates the conda environment to run BirdNET

conda activate pybirdanalyze

This will activate the conda environment

pip install --upgrade pip

This will create an installer to install the needed BirdNET extensions more smoothly

pip install tensorflow pip install librosa pip install numpy==1.20 pip install birdnetlib pip install pandas pip install xlsxwriter pip install datetime

Those last few commands will download the extensions so that we can start running BirdNET

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And with that you should be done with the hardest part of setting up Bird-Scanner.

D) Download or git clone the Bird-Scanner Repository.

If you do not understand github and its uses with R watch this quick video.

I would recommend downloading bird-scanner into you documents folder. From there, open RStudio and open the Bird_Scanner.Rproj.

In the repository, under the “code” folder open the “setup_env.R” file and change the path for the

Sys.setenv(RETICULATE_PYTHON = "C:/Users/jkauphusman/Anaconda3/envs/pybirdanalyze/python.exe")

to the paths on your computer, based on your username, of where your conda env is located. Then run the script.. Remember to keep this “setup_env.R” script within your repository so you can call to it when you run “bird_scanner.R”.

Now install the following packages so that you have no issues with the Bird-Scanner-Workflow:

install.packages(c("reticulate", "tidyverse", "devtools", "glue", "openxlsx", "readxl", "tuneR", "ggplot2", "umap", "seewave", "phonTools", "signal", "warbleR"))

If there are no errors, you should be able to run the bird_scanner.R script.

6. Run Bird-Scanner

Below, is an example and tutorial to show you how Bird-Scanner is operated following the collection of audio files from your deployed ARU. When I run my calls following a field session, I will use the bird_scanner.R script, found within the code folder of the Bird-Scanner Repository, which will auto-ID bird calls within the recordings, and output the results in a excel table format that will include: species, time of call, model prediction percentage, and when in the recording the model heard the call. For each session with bird_scanner.R all I change is the filepaths, location information, and confidence thresholds.

\(~\) If you remember at this point of the workflow, we have collected audio files at my bird feeder and loaded the wav files to my computer. After that we verified the files contained the proper date fromat YYMMDD_HHMMSS.

Here is an example of one of those recordings at the bird-feeder:

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Lets look at how the file names of the recordings should look like:

files <- list.files("./data/", recursive = TRUE, full.names = FALSE)
file_names <- data.frame(files[1:5])
knitr::kable(file_names, format = "html", caption = "Recording Filenames")

Referring to the bird-scanner.R script, I will walk through the necessary steps to run BirdNET on our gathered recordings.

First, run the setup_env.R script and then load in the filepath and designate an output folder. The setup_env.R script is needed to activate your conda environment. If you are confused with the glue() function, it essentially pastes in text based on the saved object with the {}. So below if I run

data <-glue("{path}data) it saves data as “C:/Users/jkauphusman/Desktop/Scripts/Bird_Scanner/data”, which for this tutorial all my wav files are saved under the data folder in the Bird-Scanner Repository.

Anywho, lets run the following code:

# Load in the Birdnet conda environment
source("./code/setup_env.R")
# set the file path
path <- "C:/Users/jkauphusman/Desktop/Scripts/Bird_Scanner/"
# Load in the file path of where the data is located, you will need the entire path
data <- glue("{path}data")

Now, you need to identify where your ARUs were deployed, which the coordinates will need to be in lat-long format. The BirdNET model will use these coordinates to reduce the amount of species it can use to predict based on the range data for birds identified by the Cornell Labs of Ornithology and eBird.

latitude <- 33.273595
longitude <- -111.829824

Another prerequisite is to define the confidence threshold that you want BirdNet to abide to. There are various strengths and weaknesses for a higher or lower threshold, so if you want to reduce false positives or false negatives based on your analysis you’ll need to decide what threshold is best for you. I have designated 70% to decrease false positives so that when the model is making a prediction it is very accurate.

conf <- 0.7

With those prerequisites out of the way, we can run the audio files through the BirdNET Model.

source("./code/bird_analyzer.R")
bird_analyzer(data=data, latitude=latitude, longitude=longitude, conf=conf)

## NULL

If you are using this repository, the results would be saved in the results_tables folder. In the newly outputed excel file it will be labeled birdNET_results_DATE.xlsx, and contain two sheets, the first titled Detections will be the birdNET predicted results based on the provided audio data, the second sheet titled SpeciesList will be the potential species (i.e., the greater Phoenix, AZ area) that would occur based on the geographic location from the provided audio files.

Below are the first 5 predictions from BirdNET from our Bird-feeder recordings.

Below are the species listed in the geographic area.

Again, all these steps on running BirdNET on your ARU calls should be ran through your version of the bird-scanner.R script that is provided in the Bird-Scanner Repository.

7. Check Predictions

Let’s say you ran BirdNET, and it predicted a species like “House finch” and you wanted to make sure that specific prediction was correct, here in the Bird-Scanner Workflow repository, I wrote some functions to extract a segment of the audio file when exactly in the given audio segment the model predicted the species and how to convert the audio into a spectrogram. To see how I typically run this code, in the Bird-Scanner Repository under the code folder check out the bird_checker.R script, which will give you a template on how to verify the model’s predictions. So, if you want to look at just the “House Finch” calls you can extract those results.

### What species or observation do you want to verify?

species <- "House Finch"

# create a sub table of the calls you want to investigate, lets just take the first five entries
verify <- results[1:3,] %>% 
  filter(common_name == glue("{species}"))

Then using the bird_verify function I developed for this workflow, you can output the audio segments of when the model predicted “House Finch” to the checker folder in the repository, and quickly listen to the audio segments.

# Read in the bird_verify function
source("./code/bird_verify.R")
# execute the function to the sub-table of house finch calls
bird_verify(verify)
# now check the outputs in the checker folder

Here is the example of the audio segment of the first predicted House Finch call

As you can see the model predicted correctly. If you wanted further verification, using the bird_checker.R script in the code folder you can output the spectrograms of the predicted audio segment using the bird_spec function. This function will create spectrograms for all the species you want to verify, and output the spectrograms as PNG files in the spectrograms folder of the Bird-Scanner Repository.

# Read in the bird_verify function
source("./code/bird_spec.R")
# execute the function to the sub-table of house finch calls
bird_spec(verify)
# now check the outputs in the checker folder

And there is the first prediction of the house finch in a spectrogram of when the model made the prediction. Just some backrground information, the function buffers out the predicted call by one second at the start and end of the prediction, so below in the spectrogram the model identified the call at seconds 1-4s.

Before you run bird_checker.R again, make sure to delete the wav and png files in both the checker and spectrograms folder.

8. Final Thoughts

With that, I leave you with a step-by-step tutorial of the Bird-Scanner workflow, which will give you everything you need to set up your workflow with the Bird-Scanner Repository.

I hope you will find the great applicability of using BirdNET for your avian species analyses, including the use of this workflow for various avian ESA species surveys.

If you have any questions feel free to leave a comment in the issues section of the Bird-Scanner Repository or contact me directly.

THANK YOU!!